Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.jobs.runners.chronos

import functools
import logging
import os

from galaxy import model
from galaxy.jobs.runners import (
    AsynchronousJobRunner,
    AsynchronousJobState,
)
from galaxy.util import unicodify

CHRONOS_IMPORT_MSG = (
    "The Python 'chronos' package is required to use "
    "this feature, please install it or correct the "
    "following error:\nImportError {msg!s}"
)

try:
    import chronos

    chronos_exceptions = (
        chronos.ChronosAPIError,
        chronos.UnauthorizedError,
        chronos.MissingFieldError,
        chronos.OneOfViolationError,
    )
except ImportError as e:
    chronos = None
    CHRONOS_IMPORT_MSG.format(msg=unicodify(e))


__all__ = ("ChronosJobRunner",)
LOGGER = logging.getLogger(__name__)


class ChronosRunnerException(Exception):
    pass


def handle_exception_call(func):
    # Catch chronos exceptions. The latest version of chronos-python does
    # support a hierarchy over the exceptions.

    @functools.wraps(func)
    def wrapper(*args, **kwargs):
        try:
            return func(*args, **kwargs)
        except chronos_exceptions as e:
            LOGGER.error(unicodify(e))

    return wrapper


def to_dict(segments, v):
    if len(segments) == 0:
        return v
    return {segments[0]: to_dict(segments[1:], v)}


def _write_logfile(logfile, msg):
    with open(logfile, "w") as fil:
        fil.write(msg)


def _parse_job_volumes_list(li):
    # Convert comma separated string to list
    volume_list = list(li.split(","))
    # Create the list with right mountpoint and permissions
    mountpoint_list = []
    # Convert each element to right format
    for i in volume_list:
        hpath, cpath, mode = i.split(":")
        mountpoint_list.append({"hostPath": hpath, "containerPath": cpath, "mode": mode})
    return mountpoint_list


def _add_galaxy_environment_variables(cpus, memory):
    # Set:
    # GALAXY_SLOTS: to docker_cpu
    # GALAXY_MEMORY_MB to docker_memory
    return [{"name": "GALAXY_SLOTS", "value": cpus}, {"name": "GALAXY_MEMORY_MB", "value": memory}]


[docs]class ChronosJobRunner(AsynchronousJobRunner): runner_name = "ChronosRunner" RUNNER_PARAM_SPEC_KEY = "runner_param_specs" JOB_NAME_PREFIX = "galaxy-chronos-" RUNNER_PARAM_SPEC = { "chronos": { "map": str, }, "insecure": { "map": lambda x: x in ["true", "True", "TRUE"], "default": True, }, "username": { "map": str, }, "password": { "map": str, }, "owner": {"map": str}, } DESTINATION_PARAMS_SPEC = { "docker_cpu": { "default": 0.1, "map_name": "cpus", "map": float, }, "docker_memory": { "default": 128, "map_name": "mem", "map": int, }, "docker_disk": { "default": 256, "map_name": "disk", "map": int, }, "volumes": { "default": None, "map_name": "container/volumes", "map": (lambda x: _parse_job_volumes_list(x) if x is not None else []), }, "max_retries": { "default": 2, "map_name": "retries", "map": int, }, }
[docs] def __init__(self, app, nworkers, **kwargs): """Initialize this job runner and start the monitor thread""" assert chronos, CHRONOS_IMPORT_MSG if self.RUNNER_PARAM_SPEC_KEY not in kwargs: kwargs[self.RUNNER_PARAM_SPEC_KEY] = {} kwargs[self.RUNNER_PARAM_SPEC_KEY].update(self.RUNNER_PARAM_SPEC) super().__init__(app, nworkers, **kwargs) protocol = "http" if self.runner_params.get("insecure", True) else "https" self._chronos_client = chronos.connect( self.runner_params["chronos"], username=self.runner_params.get("username"), password=self.runner_params.get("password"), proto=protocol, )
[docs] @handle_exception_call def queue_job(self, job_wrapper): LOGGER.debug(f"Starting queue_job for job {job_wrapper.get_id_tag()}") if not self.prepare_job(job_wrapper, include_metadata=False, modify_command_for_container=False): LOGGER.debug(f"Not ready {job_wrapper.get_id_tag()}") return job_destination = job_wrapper.job_destination chronos_job_spec = self._get_job_spec(job_wrapper) job_name = chronos_job_spec["name"] self._chronos_client.add(chronos_job_spec) ajs = AsynchronousJobState( files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper, job_id=job_name, job_destination=job_destination, ) self.monitor_queue.put(ajs)
[docs] @handle_exception_call def stop_job(self, job_wrapper): job_id = job_wrapper.get_id_tag() job_name = self.JOB_NAME_PREFIX + job_id job = self._retrieve_job(job_name) if job: msg = "Job {name!r} is terminated" self._chronos_client.delete(job_name) LOGGER.debug(msg.format(name=job_name)) else: msg = "Job {name!r} not found. It cannot be terminated." LOGGER.error(msg.format(name=job_name))
[docs] def recover(self, job, job_wrapper): msg = "(name!r/runner!r) is still in {state!s} state, adding to" " the runner monitor queue" job_id = job.get_job_runner_external_id() ajs = AsynchronousJobState( files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper, job_id=self.JOB_NAME_PREFIX + str(job_id), job_destination=job_wrapper.job_destination, ) ajs.command_line = job.command_line if job.state in (model.Job.states.RUNNING, model.Job.states.STOPPED): LOGGER.debug(msg.format(name=job.id, runner=job.job_runner_external_id, state=job.state)) ajs.old_state = model.Job.states.RUNNING ajs.running = True self.monitor_queue.put(ajs) elif job.state == model.Job.states.QUEUED: LOGGER.debug(msg.format(name=job.id, runner=job.job_runner_external_id, state="queued")) ajs.old_state = model.Job.states.QUEUED ajs.running = False self.monitor_queue.put(ajs)
[docs] @handle_exception_call def check_watched_item(self, job_state): job_name = job_state.job_id job = self._retrieve_job(job_name) # TODO: how can stopped GxIT jobs be handled here? if job: succeeded = job["successCount"] errors = job["errorCount"] if succeeded > 0: return self._mark_as_successful(job_state) elif not succeeded and not errors: return self._mark_as_active(job_state) elif errors: max_retries = job["retries"] if max_retries == 0: msg = "Job {name!r} failed. No retries performed." else: msg = "Job {name!r} failed more than {retries!s} times." reason = msg.format(name=job_name, retries=str(max_retries)) return self._mark_as_failed(job_state, reason) reason = f"Job {job_name!r} not found" return self._mark_as_failed(job_state, reason)
def _mark_as_successful(self, job_state): msg = "Job {name!r} finished successfully" _write_logfile(job_state.output_file, msg.format(name=job_state.job_id)) _write_logfile(job_state.error_file, "") job_state.running = False job_state.job_wrapper.change_state(model.Job.states.OK) self.mark_as_finished(job_state) return None def _mark_as_active(self, job_state): job_state.running = True job_state.job_wrapper.change_state(model.Job.states.RUNNING) return job_state def _mark_as_failed(self, job_state, reason): _write_logfile(job_state.error_file, reason) job_state.running = False job_state.stop_job = True job_state.job_wrapper.change_state(model.Job.states.ERROR) job_state.fail_message = reason self.mark_as_failed(job_state) return None
[docs] @handle_exception_call def finish_job(self, job_state): super().finish_job(job_state) self._chronos_client.delete(job_state.job_id)
[docs] def parse_destination_params(self, params): parsed_params = {} for k, spec in self.DESTINATION_PARAMS_SPEC.items(): value = params.get(k, spec.get("default")) map_to = spec.get("map_name") mapper = spec.get("map") segments = map_to.split("/") parsed_params.update(to_dict(segments, mapper(value))) return parsed_params
[docs] def write_command(self, job_wrapper): # Create command script instead passing it in the container # preventing wrong characters parsing. if not os.path.exists(job_wrapper.working_directory): LOGGER.error("No working directory found") path = f"{job_wrapper.working_directory}/chronos_{job_wrapper.get_id_tag()}.sh" mode = 0o755 with open(path, "w", encoding="utf-8") as f: f.write("#!/bin/bash\n") f.write(job_wrapper.runner_command_line) os.chmod(path, mode) return path
def _get_job_spec(self, job_wrapper): job_name = self.JOB_NAME_PREFIX + job_wrapper.get_id_tag() job_destination = job_wrapper.job_destination command_script_path = self.write_command(job_wrapper) template = { "async": False, # 'command': job_wrapper.runner_command_line, "command": f"$SHELL {command_script_path}", "owner": self.runner_params["owner"], "disabled": False, "schedule": "R1//PT1S", "name": job_name, # Add Galaxy environemnt variables to json "environmentVariables": _add_galaxy_environment_variables( job_destination.params.get("docker_cpu"), job_destination.params.get("docker_memory") ), } if not job_destination.params.get("docker_enabled"): raise ChronosRunnerException("ChronosJobRunner needs 'docker_enabled' to be set as True") destination_params = self.parse_destination_params(job_destination.params) template.update(destination_params) template["container"]["type"] = "DOCKER" template["container"]["image"] = self._find_container(job_wrapper).container_id # Fix the working directory inside the container template["container"]["parameters"] = [{"key": "workdir", "value": job_wrapper.working_directory}] return template def _retrieve_job(self, job_id): jobs = self._chronos_client.list() job = [x for x in jobs if x["name"] == job_id] if len(job) > 1: msg = f"Multiple jobs found with name {job_id!r}" LOGGER.error(msg) raise ChronosRunnerException(msg) return job[0] if job else None